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Yorodumi- PDB-5if8: Crystal structure of polymerase acid protein (PA) from Influenza ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5if8 | ||||||
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Title | Crystal structure of polymerase acid protein (PA) from Influenza A virus, WILSON-SMITH/1933 (H1N1) bound to fragment hit EBSI-2643 5-[(4-chlorophenyl)methyl]-1,3,4-oxadiazol-2-amine | ||||||
Components | Polymerase acidic protein | ||||||
Keywords | VIRAL PROTEIN / NIAID / structural genomics / flu / fragment screening / STD NMR / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Function and homology information RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds ...RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral translational frameshifting / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To Be Published Title: Fragment screening by STD NMR identifies novel site binders against influenza A virus polymerase PA Authors: Pierce, P. / Muruthi, M.M. / Abendroth, J. / Moen, S.O. / Begley, D.W. / Davies, D.R. / Marathias, V.M. / Staker, B.L. / Myler, P.J. / Lorimer, D.D. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5if8.cif.gz | 179.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5if8.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 5if8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5if8_validation.pdf.gz | 475.8 KB | Display | wwPDB validaton report |
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Full document | 5if8_full_validation.pdf.gz | 477.2 KB | Display | |
Data in XML | 5if8_validation.xml.gz | 17 KB | Display | |
Data in CIF | 5if8_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/5if8 ftp://data.pdbj.org/pub/pdb/validation_reports/if/5if8 | HTTPS FTP |
-Related structure data
Related structure data | 5ieqC 5if2C 5if5C 5if7C 5ifbC 5ifcC 5ifdC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53096.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Wilson-Smith/1933 H1N1) Strain: A/Wilson-Smith/1933 H1N1 / Gene: PA / Production host: Escherichia coli (E. coli) / References: UniProt: P15659 |
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-Non-polymers , 6 types, 102 molecules
#2: Chemical | ChemComp-6AX / |
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#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-EDO / |
#6: Chemical | ChemComp-GOL / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.71 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20 mg/mL protein against Morpheus screen condition A2 10% PEG 8000, 20% EG, 0.03 M each divalent cation, 0.1 M MES/imidazole pH 6.5, crystal tracking ID 254988a2, unique puck ID wbm4-4 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.99985 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 14, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99985 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→41.025 Å / Num. obs: 25953 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 47.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Net I/σ(I): 29.97 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2.3→41.025 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 20.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.03 Å2 / Biso mean: 59.2954 Å2 / Biso min: 25.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→41.025 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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